Gene Ontology over-representation analysis — go

Runs a GO over-representation test (via clusterProfiler::enrichGO()) on the top-ranked genes of a marker table, and either plots the top terms or returns the full result.

Usage

go_enrichment(
  markers,
  topn = 1000,
  org = c("human", "mouse"),
  title.var = "",
  plot = TRUE,
  ontology.type = "BP",
  ...
)

Arguments

markers: Data frame with a gene (SYMBOL) column and an FDR column.
topn: Number of top genes (by FDR) to test.
org: Either "human" or "mouse".
title.var: Plot title.
plot: If TRUE, return a ggplot of the top terms; if FALSE, return the enrichResult object.
ontology.type: GO ontology to test: "BP", "MF", or "CC".
...: Further arguments passed to clusterProfiler::enrichGO().

Value

A ggplot (if plot = TRUE) or a clusterProfiler enrichResult.

Examples

if (FALSE) { # \dontrun{
go_enrichment(my_markers, org = "human", ontology.type = "BP")
} # }